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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-09-13, 01:01 CEST based on data in: /home/teameinstein/Mary/SA_Polony_project/qc/trimmed_qc

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        General Statistics

        Showing 222/222 rows and 4/6 columns.
        Sample NameDupsGCAvg lenMedian lenFailedSeqs
        SRR27013147_1
        32.7%
        41.0%
        245bp
        294bp
        9%
        0.9M
        SRR27013147_2
        29.6%
        41.0%
        244bp
        294bp
        18%
        0.9M
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        32.7%
        41.0%
        245bp
        294bp
        9%
        0.9M
        SRR27013147_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        29.6%
        41.0%
        244bp
        294bp
        18%
        0.9M
        SRR27013245_1
        17.8%
        46.0%
        277bp
        301bp
        18%
        0.6M
        SRR27013245_2
        15.7%
        46.0%
        277bp
        301bp
        18%
        0.6M
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        17.8%
        46.0%
        277bp
        301bp
        18%
        0.6M
        SRR27013245_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        15.7%
        46.0%
        277bp
        301bp
        18%
        0.6M
        SRR27013246_1
        24.9%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013246_2
        21.5%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        24.9%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013246_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.5%
        41.0%
        279bp
        301bp
        9%
        0.5M
        SRR27013247_1
        21.4%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013247_2
        18.0%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        21.4%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013247_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        18.0%
        40.0%
        287bp
        301bp
        9%
        0.4M
        SRR27013248_1
        27.9%
        41.0%
        269bp
        301bp
        9%
        0.6M
        SRR27013248_2
        25.5%
        41.0%
        269bp
        301bp
        9%
        0.6M
        SRR27013249_1
        23.8%
        40.0%
        272bp
        301bp
        9%
        0.5M
        SRR27013249_2
        21.0%
        40.0%
        272bp
        301bp
        9%
        0.5M
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        23.8%
        40.0%
        272bp
        301bp
        9%
        0.5M
        SRR27013249_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        21.0%
        40.0%
        272bp
        301bp
        9%
        0.5M
        SRR27013250_1
        28.1%
        40.0%
        273bp
        301bp
        9%
        0.7M
        SRR27013250_2
        25.7%
        40.0%
        273bp
        301bp
        9%
        0.7M
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        28.1%
        40.0%
        273bp
        301bp
        9%
        0.7M
        SRR27013250_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.7%
        40.0%
        273bp
        301bp
        9%
        0.7M
        SRR27013251_1
        30.6%
        42.0%
        285bp
        301bp
        18%
        0.5M
        SRR27013251_2
        27.4%
        42.0%
        285bp
        301bp
        18%
        0.5M
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        30.6%
        42.0%
        285bp
        301bp
        18%
        0.5M
        SRR27013251_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        27.4%
        42.0%
        285bp
        301bp
        18%
        0.5M
        SRR27013252_1
        28.2%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013252_2
        25.4%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013252_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        28.2%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013252_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        25.4%
        41.0%
        273bp
        301bp
        9%
        0.6M
        SRR27013253_1
        22.6%
        40.0%
        286bp
        301bp
        9%
        0.5M
        SRR27013253_2
        19.5%
        40.0%
        286bp
        301bp
        9%
        0.5M
        SRR27013254_1
        25.3%
        40.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013254_2
        22.8%
        41.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        25.3%
        40.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013254_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        22.8%
        41.0%
        272bp
        301bp
        9%
        0.6M
        SRR27013255_1
        23.3%
        40.0%
        245bp
        294bp
        9%
        0.6M
        SRR27013255_2
        20.0%
        41.0%
        245bp
        301bp
        9%
        0.6M
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        23.3%
        40.0%
        245bp
        294bp
        9%
        0.6M
        SRR27013255_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        20.0%
        41.0%
        245bp
        301bp
        9%
        0.6M
        SRR27013256_1
        24.5%
        40.0%
        269bp
        301bp
        9%
        0.6M
        SRR27013256_2
        22.0%
        40.0%
        269bp
        301bp
        9%
        0.6M
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_1
        5.9%
        40.0%
        268bp
        301bp
        9%
        0.1M
        SRR27013256_Genome_Sequencing_of_Listeria_monocytogenes_SA_outbreak_2017_2
        5.3%
        40.0%
        268bp
        301bp
        9%
        0.1M
        SRR27013257_1
        21.8%
        40.0%
        282bp
        301bp
        9%
        0.5M
        SRR27013257_2
        17.4%
        40.0%
        282bp
        301bp
        9%
        0.5M
        SRR27013258_1
        22.4%
        40.0%
        277bp
        301bp
        9%
        0.5M
        SRR27013258_2
        18.8%
        40.0%
        277bp
        301bp
        9%
        0.5M
        SRR27013259_1
        21.3%
        40.0%
        282bp
        301bp
        9%
        0.5M
        SRR27013259_2
        16.3%
        40.0%
        282bp
        301bp
        9%
        0.5M
        SRR27013260_1
        25.4%
        40.0%
        276bp
        301bp
        9%
        0.6M
        SRR27013260_2
        21.0%
        41.0%
        276bp
        301bp
        9%
        0.6M
        SRR27013261_1
        26.6%
        41.0%
        246bp
        294bp
        9%
        0.6M
        SRR27013261_2
        23.5%
        41.0%
        246bp
        294bp
        9%
        0.6M
        SRR27013262_1
        25.5%
        40.0%
        275bp
        301bp
        9%
        0.6M
        SRR27013262_2
        21.4%
        40.0%
        275bp
        301bp
        9%
        0.6M
        SRR27013263_1
        27.1%
        41.0%
        251bp
        294bp
        9%
        0.7M
        SRR27013263_2
        24.1%
        41.0%
        251bp
        301bp
        9%
        0.7M
        SRR27013264_1
        27.4%
        40.0%
        252bp
        301bp
        9%
        0.7M
        SRR27013264_2
        22.4%
        41.0%
        251bp
        301bp
        9%
        0.7M
        SRR27013265_1
        34.8%
        41.0%
        238bp
        274bp
        9%
        1.1M
        SRR27013265_2
        31.3%
        41.0%
        238bp
        274bp
        18%
        1.1M
        SRR27013266_1
        32.3%
        41.0%
        251bp
        301bp
        9%
        0.9M
        SRR27013266_2
        27.8%
        41.0%
        251bp
        301bp
        18%
        0.9M
        SRR27013267_1
        31.0%
        41.0%
        244bp
        284bp
        9%
        0.8M
        SRR27013267_2
        29.0%
        41.0%
        244bp
        284bp
        9%
        0.8M
        SRR27013268_1
        35.6%
        40.0%
        215bp
        234bp
        18%
        1.3M
        SRR27013268_2
        32.9%
        40.0%
        215bp
        234bp
        27%
        1.3M
        SRR27013269_1
        28.7%
        41.0%
        248bp
        294bp
        18%
        0.7M
        SRR27013269_2
        25.9%
        41.0%
        248bp
        294bp
        27%
        0.7M
        SRR27013270_1
        18.4%
        40.0%
        281bp
        301bp
        9%
        0.4M
        SRR27013270_2
        15.4%
        40.0%
        281bp
        301bp
        9%
        0.4M
        SRR27013271_1
        28.7%
        41.0%
        242bp
        284bp
        9%
        0.8M
        SRR27013271_2
        24.9%
        41.0%
        242bp
        284bp
        18%
        0.8M
        SRR27013272_1
        25.9%
        41.0%
        242bp
        294bp
        9%
        0.7M
        SRR27013272_2
        23.3%
        41.0%
        241bp
        294bp
        9%
        0.7M
        SRR27013273_1
        34.4%
        41.0%
        258bp
        301bp
        9%
        0.9M
        SRR27013273_2
        30.2%
        41.0%
        258bp
        301bp
        18%
        0.9M
        SRR27013274_1
        32.2%
        41.0%
        232bp
        274bp
        9%
        1.0M
        SRR27013274_2
        27.9%
        41.0%
        232bp
        274bp
        9%
        1.0M
        SRR27013275_1
        33.8%
        41.0%
        231bp
        264bp
        9%
        1.1M
        SRR27013275_2
        31.3%
        41.0%
        231bp
        264bp
        9%
        1.1M
        SRR27013276_1
        28.3%
        41.0%
        243bp
        294bp
        9%
        0.7M
        SRR27013276_2
        25.2%
        41.0%
        243bp
        294bp
        9%
        0.7M
        SRR27013277_1
        22.9%
        40.0%
        278bp
        301bp
        9%
        0.5M
        SRR27013277_2
        18.8%
        40.0%
        278bp
        301bp
        9%
        0.5M
        SRR27013278_1
        28.0%
        41.0%
        263bp
        301bp
        9%
        0.7M
        SRR27013278_2
        23.5%
        41.0%
        263bp
        301bp
        9%
        0.7M
        SRR27013279_1
        26.4%
        41.0%
        277bp
        301bp
        9%
        0.6M
        SRR27013279_2
        20.9%
        41.0%
        277bp
        301bp
        9%
        0.6M
        SRR27013280_1
        30.2%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013280_2
        25.8%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013281_1
        19.8%
        40.0%
        283bp
        301bp
        9%
        0.4M
        SRR27013281_2
        17.1%
        40.0%
        283bp
        301bp
        9%
        0.4M
        SRR27013282_1
        28.3%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013282_2
        23.7%
        41.0%
        265bp
        301bp
        9%
        0.7M
        SRR27013283_1
        34.1%
        41.0%
        237bp
        274bp
        9%
        1.0M
        SRR27013283_2
        31.3%
        41.0%
        236bp
        274bp
        9%
        1.0M
        SRR27013284_1
        34.5%
        41.0%
        239bp
        284bp
        9%
        1.0M
        SRR27013284_2
        30.7%
        41.0%
        239bp
        284bp
        9%
        1.0M
        SRR27013285_1
        32.5%
        41.0%
        237bp
        274bp
        9%
        0.9M
        SRR27013285_2
        28.5%
        41.0%
        237bp
        274bp
        9%
        0.9M
        SRR27013286_1
        31.9%
        41.0%
        249bp
        294bp
        9%
        0.9M
        SRR27013286_2
        27.4%
        41.0%
        249bp
        294bp
        9%
        0.9M
        SRR27013287_1
        24.9%
        40.0%
        271bp
        301bp
        9%
        0.6M
        SRR27013287_2
        21.0%
        40.0%
        271bp
        301bp
        9%
        0.6M
        SRR27013288_1
        23.4%
        40.0%
        273bp
        301bp
        9%
        0.5M
        SRR27013288_2
        19.4%
        41.0%
        273bp
        301bp
        9%
        0.5M
        SRR27013289_1
        29.3%
        41.0%
        266bp
        301bp
        9%
        0.7M
        SRR27013289_2
        24.1%
        41.0%
        266bp
        301bp
        9%
        0.7M
        SRR27013290_1
        30.6%
        41.0%
        244bp
        294bp
        9%
        0.8M
        SRR27013290_2
        26.9%
        41.0%
        244bp
        294bp
        9%
        0.8M
        SRR27013291_1
        32.2%
        41.0%
        230bp
        274bp
        9%
        1.0M
        SRR27013291_2
        29.0%
        41.0%
        230bp
        264bp
        9%
        1.0M
        SRR27013292_1
        21.8%
        40.0%
        284bp
        301bp
        9%
        0.4M
        SRR27013292_2
        17.9%
        40.0%
        284bp
        301bp
        9%
        0.4M
        SRR27013293_1
        33.3%
        41.0%
        243bp
        284bp
        9%
        1.0M
        SRR27013293_2
        30.3%
        41.0%
        243bp
        284bp
        9%
        1.0M
        SRR27013294_1
        32.7%
        41.0%
        237bp
        274bp
        9%
        1.0M
        SRR27013294_2
        27.0%
        41.0%
        237bp
        274bp
        9%
        1.0M
        SRR27013295_1
        26.4%
        41.0%
        237bp
        284bp
        9%
        0.7M
        SRR27013295_2
        23.6%
        41.0%
        237bp
        284bp
        9%
        0.7M
        SRR27013296_1
        23.7%
        41.0%
        242bp
        294bp
        9%
        0.5M
        SRR27013296_2
        20.6%
        41.0%
        241bp
        294bp
        9%
        0.5M
        SRR27013297_1
        28.4%
        41.0%
        226bp
        264bp
        9%
        0.8M
        SRR27013297_2
        24.6%
        41.0%
        227bp
        264bp
        9%
        0.8M
        SRR27013298_1
        25.1%
        40.0%
        222bp
        244bp
        9%
        0.8M
        SRR27013298_2
        24.9%
        41.0%
        222bp
        244bp
        9%
        0.8M
        SRR27013299_1
        28.5%
        41.0%
        222bp
        254bp
        9%
        0.8M
        SRR27013299_2
        24.4%
        41.0%
        222bp
        254bp
        9%
        0.8M
        SRR27013300_1
        23.9%
        41.0%
        239bp
        274bp
        9%
        0.7M
        SRR27013300_2
        23.7%
        41.0%
        239bp
        274bp
        9%
        0.7M
        SRR27013301_1
        26.8%
        40.0%
        227bp
        264bp
        9%
        0.7M
        SRR27013301_2
        23.0%
        41.0%
        228bp
        264bp
        9%
        0.7M
        SRR27013302_1
        27.2%
        40.0%
        219bp
        244bp
        9%
        0.8M
        SRR27013302_2
        23.5%
        41.0%
        220bp
        244bp
        9%
        0.8M
        SRR27013303_1
        27.6%
        40.0%
        226bp
        254bp
        9%
        0.8M
        SRR27013303_2
        23.4%
        41.0%
        227bp
        254bp
        9%
        0.8M
        SRR27013304_1
        31.7%
        41.0%
        222bp
        254bp
        9%
        1.0M
        SRR27013304_2
        27.7%
        41.0%
        222bp
        254bp
        9%
        1.0M
        SRR27013305_1
        20.9%
        41.0%
        248bp
        294bp
        9%
        0.5M
        SRR27013305_2
        19.7%
        41.0%
        249bp
        301bp
        9%
        0.5M
        SRR27013306_1
        23.8%
        41.0%
        216bp
        234bp
        9%
        0.7M
        SRR27013306_2
        24.1%
        41.0%
        217bp
        234bp
        9%
        0.7M
        SRR27013307_1
        23.6%
        41.0%
        256bp
        294bp
        9%
        0.6M
        SRR27013307_2
        19.6%
        41.0%
        257bp
        294bp
        9%
        0.6M
        SRR27013308_1
        22.9%
        40.0%
        237bp
        274bp
        9%
        0.6M
        SRR27013308_2
        22.4%
        41.0%
        238bp
        274bp
        9%
        0.6M
        SRR27013309_1
        23.9%
        41.0%
        238bp
        274bp
        9%
        0.6M
        SRR27013309_2
        22.6%
        41.0%
        239bp
        284bp
        9%
        0.6M
        SRR27013310_1
        22.1%
        40.0%
        225bp
        254bp
        27%
        0.6M
        SRR27013310_2
        22.4%
        41.0%
        225bp
        254bp
        18%
        0.6M
        SRR27013311_1
        22.6%
        41.0%
        235bp
        274bp
        9%
        0.6M
        SRR27013311_2
        21.7%
        41.0%
        236bp
        274bp
        9%
        0.6M
        SRR27013312_1
        22.3%
        40.0%
        245bp
        294bp
        9%
        0.5M
        SRR27013312_2
        21.7%
        40.0%
        245bp
        294bp
        18%
        0.5M
        SRR27013313_1
        24.3%
        40.0%
        248bp
        294bp
        9%
        0.6M
        SRR27013313_2
        23.6%
        41.0%
        247bp
        294bp
        18%
        0.6M
        SRR27013314_1
        26.0%
        40.0%
        226bp
        254bp
        9%
        0.8M
        SRR27013314_2
        25.5%
        41.0%
        227bp
        254bp
        9%
        0.8M
        SRR27013315_1
        25.9%
        41.0%
        239bp
        264bp
        9%
        0.7M
        SRR27013315_2
        24.1%
        41.0%
        239bp
        264bp
        9%
        0.7M
        SRR27013316_1
        24.0%
        40.0%
        240bp
        274bp
        9%
        0.7M
        SRR27013316_2
        23.7%
        41.0%
        240bp
        274bp
        9%
        0.7M
        SRR27013317_1
        25.2%
        40.0%
        241bp
        274bp
        9%
        0.7M
        SRR27013317_2
        23.1%
        40.0%
        241bp
        274bp
        9%
        0.7M
        SRR27013318_1
        21.2%
        41.0%
        260bp
        301bp
        9%
        0.5M
        SRR27013318_2
        17.4%
        41.0%
        260bp
        301bp
        9%
        0.5M
        SRR27013319_1
        19.8%
        40.0%
        247bp
        294bp
        9%
        0.5M
        SRR27013319_2
        19.3%
        41.0%
        248bp
        301bp
        9%
        0.5M
        SRR27013320_1
        24.9%
        41.0%
        236bp
        264bp
        9%
        0.7M
        SRR27013320_2
        23.4%
        41.0%
        235bp
        264bp
        9%
        0.7M
        SRR27013321_1
        25.6%
        40.0%
        234bp
        264bp
        9%
        0.7M
        SRR27013321_2
        25.4%
        41.0%
        233bp
        264bp
        18%
        0.7M
        SRR27013322_1
        27.5%
        41.0%
        240bp
        274bp
        9%
        0.8M
        SRR27013322_2
        26.2%
        41.0%
        240bp
        274bp
        9%
        0.8M
        SRR27013323_1
        21.9%
        41.0%
        237bp
        274bp
        9%
        0.6M
        SRR27013323_2
        20.3%
        41.0%
        238bp
        284bp
        9%
        0.6M
        SRR27013324_1
        24.6%
        40.0%
        240bp
        274bp
        9%
        0.7M
        SRR27013324_2
        23.7%
        41.0%
        239bp
        274bp
        9%
        0.7M
        SRR27013325_1
        27.2%
        41.0%
        236bp
        264bp
        9%
        0.7M
        SRR27013325_2
        25.9%
        41.0%
        236bp
        264bp
        9%
        0.7M
        SRR27013326_1
        23.6%
        40.0%
        235bp
        264bp
        9%
        0.7M
        SRR27013326_2
        22.6%
        40.0%
        235bp
        264bp
        9%
        0.7M
        SRR27013327_1
        24.2%
        40.0%
        249bp
        294bp
        9%
        0.6M
        SRR27013327_2
        21.4%
        40.0%
        250bp
        294bp
        9%
        0.6M
        SRR27013328_1
        25.3%
        41.0%
        240bp
        274bp
        9%
        0.6M
        SRR27013328_2
        23.4%
        41.0%
        240bp
        274bp
        9%
        0.6M
        SRR27013329_1
        28.5%
        40.0%
        235bp
        264bp
        9%
        0.8M
        SRR27013329_2
        25.3%
        41.0%
        235bp
        264bp
        18%
        0.8M
        SRR27013330_1
        30.4%
        40.0%
        244bp
        294bp
        9%
        0.9M
        SRR27013330_2
        25.8%
        41.0%
        244bp
        284bp
        18%
        0.9M
        SRR27013331_1
        30.0%
        40.0%
        241bp
        284bp
        9%
        0.9M
        SRR27013331_2
        24.9%
        40.0%
        241bp
        284bp
        9%
        0.9M
        SRR27013332_1
        28.9%
        40.0%
        243bp
        294bp
        9%
        0.8M
        SRR27013332_2
        23.8%
        40.0%
        243bp
        294bp
        9%
        0.8M
        SRR27013333_1
        31.8%
        40.0%
        247bp
        294bp
        9%
        0.9M
        SRR27013333_2
        26.2%
        40.0%
        247bp
        294bp
        9%
        0.9M
        SRR27013334_1
        33.8%
        40.0%
        239bp
        274bp
        9%
        1.1M
        SRR27013334_2
        29.0%
        41.0%
        239bp
        274bp
        9%
        1.1M
        SRR27013335_1
        29.1%
        40.0%
        240bp
        284bp
        9%
        0.8M
        SRR27013335_2
        24.8%
        40.0%
        240bp
        284bp
        9%
        0.8M
        SRR27013336_1
        29.5%
        40.0%
        245bp
        294bp
        9%
        0.8M
        SRR27013336_2
        24.5%
        41.0%
        245bp
        294bp
        18%
        0.8M
        SRR27013337_1
        30.5%
        42.0%
        255bp
        301bp
        18%
        0.7M
        SRR27013337_2
        24.7%
        42.0%
        255bp
        301bp
        18%
        0.7M
        SRR27013338_1
        30.7%
        40.0%
        266bp
        301bp
        18%
        0.6M
        SRR27013338_2
        27.6%
        40.0%
        266bp
        301bp
        18%
        0.6M
        SRR27013339_1
        27.2%
        41.0%
        254bp
        294bp
        9%
        0.7M
        SRR27013339_2
        21.8%
        41.0%
        254bp
        301bp
        9%
        0.7M
        SRR27013340_1
        25.1%
        40.0%
        279bp
        301bp
        9%
        0.6M
        SRR27013340_2
        21.7%
        40.0%
        279bp
        301bp
        9%
        0.6M
        SRR27013341_1
        35.4%
        41.0%
        233bp
        264bp
        9%
        1.1M
        SRR27013341_2
        32.5%
        41.0%
        233bp
        264bp
        9%
        1.1M
        SRR27013342_1
        31.3%
        41.0%
        246bp
        294bp
        9%
        0.9M
        SRR27013342_2
        27.9%
        41.0%
        246bp
        294bp
        9%
        0.9M
        SRR27013343_1
        40.5%
        40.0%
        227bp
        264bp
        9%
        1.0M
        SRR27013343_2
        37.1%
        41.0%
        227bp
        264bp
        9%
        1.0M

        FastQC

        Version: 0.12.1

        Quality control tool for high throughput sequencing data.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        222 samples had less than 1% of reads made up of overrepresented sequences

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 1/1 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        AACTAAAACCGATCCATCATCAAAAACAGAAATTTGAACAGGTTGATAAT
        4
        2346
        0.0015%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        FastQC0.12.1